The host recognition and invasion process of Myxobolus cerebralis actinospores (triactinomyxon, TAM) was studied on a genetic level. A small-scale in vitro assay was developed to activate a large number of TAMs simultaneously, and to monitor the host invasion in the absence of live fish. The transcriptomes of non-activated and in vitro-activated TAMs were compared by suppressive subtractive hybridization (SSH) to identify parasite genes involved in the host invasion process. Differential screening and a subsequent BLAST search revealed 15 of 452 SSH-library clones expressed differently in activated TAMs. None of the 15 transcripts obtained has previously been identified from M. cerebralis. Quantitative real-time PCR was used to examine the relative expression profile of 8 selected transcripts upon TAM activation and after penetration of the host. Four of these were found to be up-regulated in activated TAMs, while expression was relatively low in non-activated TAMs and in infected fish tissue, indicating that they are relevant genes during host recognition or subsequent host invasion of M. cerebralis TAMs.